Genome-wide classifiers for detection of subacute transplant rejection and other transplant conditions

The method of any one of the preceding claims, wherein the gene expression levels comprise levels of at least 10 genes, at least 20 genes, at least 40 genes, at least 50 genes, at least 60 genes, at least 70 genes, at least 80 genes, at least 90 genes or all of the genes in Table 3 or 4.

The method of any one of the preceding claims, wherein the method has a positive predictive value (PPV) of greater than 40%, 65%, greater than 70%, greater than 75%, greater than 80%, greater than 85%, greater than 90%, or greater than 95%.

The method of any one of the preceding claims, wherein the method has a negative predictive value (NPV) of greater than 65%, greater than 70%, greater than 75%, greater than 80%, greater than 85%, greater than 90%, or greater than 95%.

The method of any one of the preceding claims, wherein the method comprises detecting a transplant excellent condition in the kidney transplant recipient and the method further comprises administering a treatment to kidney transplant recipient based on the detected transplant excellent condition.

The method any one of the preceding claims, wherein the treatment comprises abstaining from performing a protocol biopsy of the kidney transplant of the kidney transplant recipient after the transplant excellent condition is detected in a blood sample from the kidney transplant recipient at least one time, at least two consecutive times, or at least three consecutive times.

The method of any one of the preceding claims, wherein the method comprises monitoring gene expression products in a blood sample obtained from a kidney transplant recipient on different days, wherein the markers are mRNA expression products of at least 5 genes, at least 10 genes, at least 20 genes, at least 30 genes, at least 50 genes, at least 100 genes or all of the genes from Tables 3 or 4.

The method of any one of the preceding claims, wherein the method detects a non-transplant excellent condition in the kidney transplant recipient and the method further comprises administering a treatment to the kidney transplant recipient based on the detected non-transplant excellent condition.

The method of any one of the preceding claims, wherein the method further comprises monitoring blood samples from the kidney transplant recipient in order to detect a non-transplant excellent condition.

The method of any one of the preceding claims, wherein the non-transplant condition is monitored by detecting mRNA expression levels of at least 5 genes, at least 10 genes from Tables 3 or 4 in blood samples obtained from the kidney transplant recipient on at least two or at least three different days and further comprising applying a trained algorithm to the detected expression levels in order to distinguish a transplant excellent condition from a non-transplant excellent condition.

The method of any one of the preceding claims, wherein the treatment further comprises monitoring the blood samples in order to detect subAR in the kidney transplant recipient.

The method of any one of the preceding claims, wherein the monitoring the blood samples in order to detect subAR in the kidney transplant recipient comprises detecting mRNA expression products of at least 5 genes, at least 10 genes, at least 20 genes, at least 30 genes, at least 50 genes, or all of the genes in Table 5, 6, or 8 and applying a trained algorithm to the detected mRNA expression products.

The method of any one of the preceding claims, wherein the method further comprises administering an immunosuppressant drug to the kidney transplant recipient to treat the detected subAR or the detected non-transplant excellent condition.

The method of any one of the preceding claims, further comprising administering an increased or decreased dose of the immunosuppressant drug to the kidney transplant recipient in order to treat or prevent the detected non-transplant excellent condition or detected subAR or administering a new immunosuppressant drug to the kidney transplant recipient in order to treat or prevent the detected non-transplant excellent condition or the detected subAR.

The method of any one of the preceding claims, wherein the immunosuppressant drug or the new immunosuppressant drug is a calcineurin inhibitor.

The method of any one of the preceding claims, wherein the immunosuppressant drug or the new immunosuppressant drug is an mTOR inhibitor.

The method of any one of the preceding claims, wherein the immunosuppressant drug or new immunosuppressant drug is selected from the group consisting of:

• azathioprine, leflunomide, mycophenolic acid, mycophenolate mofetil, prednisolone, hydrocortisone, basiliximab, alemtuzumab, daclizumab, belatacept, orthoclone, anti-thymocyte globulin, anti-lymphocyte globulin, an anti-proliferative drug, and an anti-T cell antibody.

The method of any one of the preceding claims, wherein the method further comprises detecting a serum creatinine level or an eGFR in a blood sample from the kidney transplant recipient.

The method of any one of the preceding claims, wherein the method further comprises using a serum creatinine level or an eGFR to further confirm the detected subAR, the detected non-transplant excellent condition, or the detected transplant excellent condition.

The method of any one of the preceding claims, wherein the kidney transplant recipient has a serum creatinine level of less than 2.3 mg/dL.

The method of any one of the preceding claims, further comprising administering an adjusted dose, an increased dose or a decreased dose of the immunosuppressant drug to the kidney transplant recipient in order to treat or prevent the detected subAR or administering a new immunosuppressant drug to the kidney transplant recipient in order to treat or prevent the detected subAR.

The method of any one of the preceding claims, wherein the treatment further comprises monitoring the blood samples in order to detect subAR or a transplant excellent condition in the kidney transplant recipient at two or more time points.

The method of any one of the preceding claims, wherein the monitoring the blood samples in order to detect subAR or a transplant excellent condition in the kidney transplant recipient comprises detecting mRNA expression products of at least 5 genes, at least 10 genes, at least 20 genes, at least 30 genes, at least 50 genes, or all of the genes in Table 5, 6, or 8.

The method any one of the preceding claims, wherein the treatment comprises abstaining from performing a protocol biopsy of the kidney transplant of the kidney transplant recipient after the transplant excellent condition is detected in a blood sample from the kidney transplant recipient at least one time, at least two consecutive times, or at least three consecutive times.

The method of any one of the preceding claims, wherein the method comprises monitoring gene expression products in a blood sample obtained from a kidney transplant recipient on different days, wherein the markers are mRNA expression products of at least 5 genes, at least 10 genes, at least 20 genes, at least 30 genes, at least 50 genes, at least 100 genes or all of the genes from Tables 5, 6, or 8.

The method of any one of the preceding claims, wherein the treatment further comprises periodically obtaining blood samples from the kidney transplant recipient and monitoring the blood samples in order to detect subAR or a transplant excellent condition in the kidney transplant recipient.

The method of any one of the preceding claims, wherein the method further comprises repeating the method at least one time, at least two times, at least three times, or at least four times in order to monitor a detected transplant excellent condition, a detected non-transplant excellent condition, or a detected sub-acute rejection, or any combination thereof in the kidney transplant recipient.

The method of any one of the preceding claims, wherein the initial immunosuppressant drug or the new immunosuppressant drug is selected from the group consisting of a calcineurin inhibitor, an mTOR inhibitor, azathioprine, leflunomide, mycophenolic acid, mycophenolate mofetil, prednisolone, hydrocortisone, basiliximab, alemtuzumab, daclizumab, belatacept, orthoclone, anti-thymocyte globulin, anti-lymphocyte globulin, an anti-proliferative drug, and an anti-T cell antibody, or a combination thereof.

The method of any one of the preceding claims, wherein the method further comprises abstaining from performing a biopsy on the kidney transplant recipient after the transplant excellent condition is identified in (d).

The method of any one of the preceding claims, wherein the method further comprises abstaining from performing a biopsy on the kidney transplant recipient after the transplant excellent condition is identified in (d) after the method is performed at least two consecutive times, at least three consecutive times, at least four consecutive times, or at least five consecutive times.

The method of any one of the preceding claims, wherein the method further comprises repeating (a), (b) and (c) at least one time, at least two times, at least three times, or at least four times over a period of days, weeks, or months.

The method of the preceding claim, wherein a subAR condition is detected using the trained algorithm in (d) after the method is performed at least two consecutive times, at least three consecutive times, at least four consecutive times, or at least five consecutive times.

The method of the preceding claim, further comprising performing a biopsy on the kidney transplant recipient after a subAR condition is detected at least two consecutive times, at least three consecutive times, at least four consecutive times, or at least five consecutive times.

The method of the preceding claim, further comprising increasing or changing the immunosuppressant drug regimen after a subAR condition is detected at least two consecutive times, at least three consecutive times, at least four consecutive times, or at least five consecutive times after the first transplant excellent condition is detected.

The method of any one of the preceding claims, further comprising treating the subAR detected by the kidney biopsy.

The method of any one of the preceding claims, further comprising contacting the gene expression products with probes, wherein the probes are specific for the at least five genes from Tables 5, 6, or 8.

The method of any one of the preceding claims, further comprising treating the non-transplant excellent condition detected by the kidney biopsy.

The method of the preceding claim, wherein the treating the detected non-transplant excellent condition comprises administering an increased or decreased dose of the immunosuppressant drug to the kidney transplant recipient in order to treat the detected non-transplant excellent condition or administering a new immunosuppressant drug to the kidney transplant recipient in order to treat the detected non-transplant excellent condition.

The method of any one of the preceding claims, wherein the method further comprises for each of the at least five genes assigning the expression level of the gene in the kidney transplant recipient a value or other designation providing an indication whether the kidney transplant recipient has or is at risk of developing subAR, has or is at risk of having acute rejection (AR), has a well-functioning normal transplant (TX), or has or is at risk of having a non-transplant excellent condition, in any combination.

The method of any one of the preceding claims, wherein the method is repeated at different times on the kidney transplant recipient, such as in weekly, monthly, two-month, or three-month intervals following introduction of the transplant into the kidney transplant recipient.

The method of any one of the preceding claims, wherein the kidney transplant recipient is receiving a drug, and a change in the combined value or designation over time provides an indication of the effectiveness of the drug.

The method of any one of the preceding claims, wherein the kidney transplant recipient has undergone a kidney transplant within 1 month, 3 months, 1 year, 2 years, 3 years or 5 years of performing (a).

The method of any one of the preceding claims, wherein the sample from the kidney transplant recipient in (a) is a blood sample and comprises whole blood, peripheral blood, serum, plasma, PBLs, PBMCs, T cells, CD4 T cells CD8 T cells, or macrophages.

The method of any one of the preceding claims, further comprising changing the treatment regime of the kidney transplant recipient responsive to the detecting step.

The method of any one of the preceding claims, wherein the kidney transplant recipient has received a drug before performing the methods, and the changing the treatment regime comprises administering an additional drug, administering a higher dose of the same drug, administering a lower dose of the same drug or stopping administering the same drug.

The method of any one of the preceding claims, further comprising performing an additional procedure to detect subAR or risk thereof if the detecting in (c) provides an indication the kidney transplant recipient has or is at risk of subAR.

The method of any one of the preceding claims, wherein the additional procedure is a kidney biopsy.

The method of any one of the preceding claims, wherein (c) is performed by a computer.

The method of any one of the preceding claims, wherein the kidney transplant recipient is human.

The method of any one of the preceding claims, wherein for each of the at least five genes, (c) comprises comparing the expression level of the gene in the kidney transplant recipient to one or more reference expression levels of the gene associated with subAR, or lack of transplant rejection (TX).

The method of any one of the preceding claims, wherein the trained algorithm is applied to expression levels of fewer than 50 genes, fewer than 80 genes, fewer than 100 genes, fewer than 150 genes, fewer than 200 genes, fewer than 300 genes, fewer than 500 genes, or fewer than 1000 genes.

The method of any one of the preceding claims, wherein the expression levels of up to 100 or up to 1000 genes are determined.

The method of any one of the preceding claims, wherein the expression levels are determined at the mRNA level or at the protein level.

The method of any one of the preceding claims, wherein the expression levels are determined by quantitative PCR, hybridization to an array or sequencing.

The method of any one of the preceding claims, further comprising contacting the nucleic acids of interest with probes, wherein the probes are specific for the at least five genes selected from Table 3, 4, 5, 6, or 8.

The method of any one of the preceding claims, comprising terminating administration of the new immunosuppressive drug after repeating (a)-(c).

The method of any one of the preceding claims, further comprising performing a microarray assay on the nucleic acids of interest obtained in (a).

The method of the preceding claim, wherein the classification is accomplished by DLDA, Nearest Centroid, Random Forest, or a Prediction Analysis of Microarrays.

The method of any one of the preceding claims, wherein the at least a two-way classifier set is obtained by ranking probe sets by p-value as to ability to distinguish between a transplant excellent kidney and a kidney with sub-acute clinical rejection.

The method of any one of the preceding claims, wherein outputting a classification for the sample comprises transmission to an end user via a computer network.

The method of any one of the preceding claims, wherein the end user is a patient from which the blood sample was derived, a physician, or a caregiver of the patient from which the sample was derived.

The method of any one of the preceding claims, wherein the computer network is the Internet, an internet or extranet, or an intranet and/or extranet that is in communication with the Internet.

The method of any one of the preceding claims, wherein transmission to an end user comprises transmission to a web-based application on a local computer or a mobile application provided to a mobile digital processing device.

The method of the preceding claim, wherein the classification is accomplished by DLDA, Nearest Centroid, Random Forest, or a Prediction Analysis of Microarrays.

The method of any one of the preceding claims, wherein the at least a two-way classifier set is obtained by ranking probe sets by p-value as to ability to distinguish between a transplant excellent kidney and a non-transplant excellent kidney.

The method of any one of the preceding claims, wherein outputting a classification for the sample comprises transmission to an end user via a computer network.

The method of any one of the preceding claims, wherein the end user is a patient from which the blood sample was derived, a physician, or a caregiver of the patient from which the sample was derived.

The method of any one of the preceding claims, wherein the computer network is the Internet, an internet and/or extranet, or an intranet and/or extranet that is in communication with the Internet.

The method of any one of the preceding claims, wherein transmission to an end user comprises transmission to a web-based application on a local computer or a mobile application provided to a mobile digital processing device.